User: Rory Stark

gravatar for Rory Stark
Rory Stark2.6k
Reputation:
2,560
Status:
Trusted
Location:
CRUK, Cambridge, UK
Last seen:
1 week ago
Joined:
5 years, 8 months ago
Email:
r*********@cruk.cam.ac.uk

I am Principal Bioinformatics Analyst at the University of Cambridge, leading the Analysis Team in the Bioinformatics Core at Cancer Research UK's Cambridge Institute.

Posts by Rory Stark

<prev • 450 results • page 1 of 45 • next >
0
votes
1
answers
89
views
1
answers
Answer: A: Differential analysis of multiple samples with different time points
... If you want to track the differences across time between two groups in a single comparison, DiffBind is not really set up to do that. You'd need to use one of the underlying analysis methods, like DESeq2, directly. There are a number of threads discussing how to set up time series analyses in DESeq2 ...
written 7 days ago by Rory Stark2.6k
0
votes
1
answers
42
views
1
answers
Answer: A: dba.report() output counts
... If you called dba.analyze() with defaults (method=DBA_DESEQ2, bFullLibrarySize=TRUE, bSubControl=TRUE), then the read counts have the control reads subtracted, are set to a minimum value of 1, and then normalized to the smallest library size. They are not reported as logs nor as RPKM values. The co ...
written 20 days ago by Rory Stark2.6k
0
votes
1
answers
99
views
1
answers
Answer: A: Blocking factors for differential binding analysis with DiffBind
... If you have normal and disease for each patient, and all the patient ChIPs (both normal and disease) were done in the same run, then the second one is correct. ...
written 20 days ago by Rory Stark2.6k
0
votes
1
answers
78
views
1
answers
Answer: A: Is there a way to run Diffbind without the normalization ?
... I am currently working on giving users much more control over normalization in DiffBind. In the meantime, there is a trick you can do you avoid normalization when using DESeq2 as the analysis method. After running dba.count(), you can change the individual library sizes to all be the same. Then if ...
written 20 days ago by Rory Stark2.6k
0
votes
1
answers
115
views
1
answers
Answer: A: DiffBind confuses coordinates of peaks
... The issue is that when you convert a GRanges object to a data.frame, the seqnames field (which contains the chromosome or contig name) becomes a factor. If you try to look at them as numbers you get a factor number, which due to the sort order used in DiffBind, does not correspond directly to the ch ...
written 21 days ago by Rory Stark2.6k
0
votes
1
answers
107
views
1
answers
Comment: C: Question of DiffBind for ChIP-Seq analysis
... The default is to use normalized counts. DBA_SCORE_READS uses non-normalized counts. ...
written 26 days ago by Rory Stark2.6k
0
votes
1
answers
115
views
1
answers
Comment: C: DiffBind confuses coordinates of peaks
... Hello- Can you email me your DBA object SU_vs_hybrid? I can have a look at what is going on. It would also help to know what version of DiffBind you are using (output of sessionInfo() -Rory ...
written 26 days ago by Rory Stark2.6k
0
votes
1
answers
106
views
1
answers
Answer: A: How to get peaks summit using dba.peakset
... You can get the summit coordinates for the full binding matrix by setting the score to DBA_SCORE_SUMMIT_POS. Here's how to do it using the example dataset: data(tamoxifen_analysis) tamoxifen <- dba.count(tamoxifen, peaks=NULL, score=DBA_SCORE_SUMMIT_POS) summitCoordinates <- dba.peakset(tamo ...
written 6 weeks ago by Rory Stark2.6k
0
votes
1
answers
202
views
1
answers
Comment: C: DiffBind MA plot
... I'll put it on the list! ...
written 11 weeks ago by Rory Stark2.6k
0
votes
1
answers
148
views
1
answers
Comment: C: DESeq2 baseMean from DiffBind summarizedExperiment
... In this case, where the count score is DBA_SCORE_READS, the binding matrix does not have pileup scores, but rather the total number of reads that align overlapping each (consensus) peak. This is similar to what you get in RNA data, where the expression matrix has the raw number of reads that overlap ...
written 11 weeks ago by Rory Stark2.6k

Latest awards to Rory Stark

Scholar 8 weeks ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Scholar 5 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Popular Question 16 months ago, created a question with more than 1,000 views. For diffbind
Scholar 16 months ago, created an answer that has been accepted. For A: DiffBind dba.analyze() to return all differentially enriched peaks?
Scholar 16 months ago, created an answer that has been accepted. For A: DiffBind matrix of values
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: Diffbind - What exactly is a "consensus" peak set?
Scholar 16 months ago, created an answer that has been accepted. For A: DiffBind - Losing replicate information?
Scholar 16 months ago, created an answer that has been accepted. For A: Error "if (is.na(peaks)) { : argument is of length zero " in DiffBind
Scholar 16 months ago, created an answer that has been accepted. For A: DiffBind MA plot
Popular Question 16 months ago, created a question with more than 1,000 views. For a diffBind problem
Scholar 16 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Scholar 16 months ago, created an answer that has been accepted. For A: MA plot DiffBind in ggplot2
Scholar 16 months ago, created an answer that has been accepted. For A: Diffbind: dba.plot retrieve variance explained
Popular Question 16 months ago, created a question with more than 1,000 views. For DiffBind Question
Popular Question 16 months ago, created a question with more than 1,000 views. For minOverlap in DiffBind in R- what does it mean?
Scholar 16 months ago, created an answer that has been accepted. For A: DiffBind Heatmap Omitting Results?
Scholar 16 months ago, created an answer that has been accepted. For A: Diffbind and dba.peakset vs dba.overlap
Scholar 16 months ago, created an answer that has been accepted. For A: What does dba.PCA in DiffBind exactly do?
Scholar 16 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Guru 17 months ago, received more than 100 upvotes.
Popular Question 17 months ago, created a question with more than 1,000 views. For a diffBind problem
Scholar 18 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Popular Question 18 months ago, created a question with more than 1,000 views. For a diffBind problem
Scholar 20 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error
Scholar 20 months ago, created an answer that has been accepted. For A: DiffBind "no lines available in input" error

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 361 users visited in the last hour